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exercises:2015_pitt:aimd

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exercises:2015_pitt:aimd [2015/03/03 12:07]
vondele [Required files]
exercises:2015_pitt:aimd [2015/03/03 12:10]
vondele [g(r)]
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 The second goal to understand the produced .ener file and do some basic analysis of the trajectory with VMD. The second goal to understand the produced .ener file and do some basic analysis of the trajectory with VMD.
  
-====== AIMD of water ======+====== AIMD of bulk liquid ​water ======
  
 <​note>​For the sake of running this exercise quickly, we'll use the DZVP-GTH basis found in the HFX_BASIS file. This basis is smaller than what can be recommended for a subtle substance such as liquid water, rather use TZV2P-GTH, TZV2P-MOLOPT-GTH,​ or cc-TZV2P or better basis sets for production runs.</​note>​ <​note>​For the sake of running this exercise quickly, we'll use the DZVP-GTH basis found in the HFX_BASIS file. This basis is smaller than what can be recommended for a subtle substance such as liquid water, rather use TZV2P-GTH, TZV2P-MOLOPT-GTH,​ or cc-TZV2P or better basis sets for production runs.</​note>​
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 How many neighbors does a given water molecule have on average (3, 3-4, 4, 4-5, 5)? How many neighbors does a given water molecule have on average (3, 3-4, 4, 4-5, 5)?
  
-=== IR spectrum ===+==== IR spectrum ​====
  
 Based on the time evolution of the dipole of the system, the IR spectral density can be estimated. To estimate the dipole from AIMD, wannier centers need to be computed. This is out of scope of the current tutorial (TODO: find link). We employ a simple approximation,​ namely classical point charges for the water molecules. In this context the approximation is reasonable. Based on the time evolution of the dipole of the system, the IR spectral density can be estimated. To estimate the dipole from AIMD, wannier centers need to be computed. This is out of scope of the current tutorial (TODO: find link). We employ a simple approximation,​ namely classical point charges for the water molecules. In this context the approximation is reasonable.
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 <​note>​ Lower frequencies need longer trajectories for reasonable estimates, at the very least 10 times the period of the signal </​note>​ <​note>​ Lower frequencies need longer trajectories for reasonable estimates, at the very least 10 times the period of the signal </​note>​
  
 +====== AIMD of simle ions in water solution ======
 ===== 4th task: simple ions in solution ===== ===== 4th task: simple ions in solution =====
  
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 The easiest way to do so is to replace one or more water molecules (depending on the size of the ion) by the ion in question. Obviously, the configuration produced in this way is far from equilibrium,​ and must be run for a while before it is representative. ​ The easiest way to do so is to replace one or more water molecules (depending on the size of the ion) by the ion in question. Obviously, the configuration produced in this way is far from equilibrium,​ and must be run for a while before it is representative. ​
  
-Entertaining is to turn one H2O in H+, do you see Eigen and Zundel states and [[wp>​Grotthuss_mechanism |the Grotthuss mechanism]] ?+Entertaining is to turn one H2O into H+, do you see Eigen and Zundel states and [[wp>​Grotthuss_mechanism |the Grotthuss mechanism]] ?
  
 ====== Required files ====== ====== Required files ======
exercises/2015_pitt/aimd.txt ยท Last modified: 2015/03/03 12:10 by vondele